HEADER CELL ADHESION 26-SEP-15 5DZW TITLE PROTOCADHERIN ALPHA 4 EXTRACELLULAR CADHERIN DOMAINS 1-4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTOCADHERIN ALPHA-4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 30-450; COMPND 5 SYNONYM: PCDH-ALPHA-4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PCDHA4, CNR1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293F KEYWDS CADHERIN, DIMER, EXTRACELLULAR, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR K.M.GOODMAN,F.BAHNA,S.MANNEPALLI,B.HONIG,L.SHAPIRO REVDAT 5 27-SEP-23 5DZW 1 HETSYN REVDAT 4 29-JUL-20 5DZW 1 COMPND JRNL REMARK HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 01-JUN-16 5DZW 1 JRNL REVDAT 2 25-MAY-16 5DZW 1 JRNL REVDAT 1 04-MAY-16 5DZW 0 JRNL AUTH K.M.GOODMAN,R.RUBINSTEIN,C.A.THU,F.BAHNA,S.MANNEPALLI, JRNL AUTH 2 G.AHLSEN,C.RITTENHOUSE,T.MANIATIS,B.HONIG,L.SHAPIRO JRNL TITL STRUCTURAL BASIS OF DIVERSE HOMOPHILIC RECOGNITION BY JRNL TITL 2 CLUSTERED ALPHA- AND BETA-PROTOCADHERINS. JRNL REF NEURON V. 90 709 2016 JRNL REFN ISSN 0896-6273 JRNL PMID 27161523 JRNL DOI 10.1016/J.NEURON.2016.04.004 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 54.9 REMARK 3 NUMBER OF REFLECTIONS : 14859 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.267 REMARK 3 R VALUE (WORKING SET) : 0.266 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 739 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.5689 - 4.1529 0.99 5189 273 0.2335 0.2613 REMARK 3 2 4.1529 - 3.2977 0.95 4874 266 0.2878 0.3035 REMARK 3 3 3.2977 - 2.8813 0.53 2740 134 0.3054 0.3572 REMARK 3 4 2.8813 - 2.6180 0.20 1025 53 0.3010 0.3551 REMARK 3 5 2.6180 - 2.4304 0.06 292 13 0.3079 0.2868 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 3221 REMARK 3 ANGLE : 0.564 4411 REMARK 3 CHIRALITY : 0.022 548 REMARK 3 PLANARITY : 0.003 572 REMARK 3 DIHEDRAL : 9.131 1161 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 1:97)) REMARK 3 ORIGIN FOR THE GROUP (A): -18.7472 19.1803 -65.4541 REMARK 3 T TENSOR REMARK 3 T11: 0.2017 T22: 0.2795 REMARK 3 T33: -0.0850 T12: 0.2430 REMARK 3 T13: 0.0058 T23: 0.0374 REMARK 3 L TENSOR REMARK 3 L11: 0.2562 L22: 0.2181 REMARK 3 L33: 0.0961 L12: -0.0488 REMARK 3 L13: -0.1575 L23: 0.0314 REMARK 3 S TENSOR REMARK 3 S11: -0.1328 S12: -0.2575 S13: -0.0271 REMARK 3 S21: 0.2212 S22: 0.1013 S23: -0.0286 REMARK 3 S31: 0.0653 S32: 0.1294 S33: -0.3566 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 98:206)) REMARK 3 ORIGIN FOR THE GROUP (A): -11.3062 20.8169 -21.1870 REMARK 3 T TENSOR REMARK 3 T11: 1.0111 T22: 1.0151 REMARK 3 T33: 0.2783 T12: 0.0686 REMARK 3 T13: -0.2239 T23: 0.1770 REMARK 3 L TENSOR REMARK 3 L11: 0.1313 L22: 0.0850 REMARK 3 L33: 0.1824 L12: 0.0133 REMARK 3 L13: -0.0131 L23: -0.0166 REMARK 3 S TENSOR REMARK 3 S11: 0.0229 S12: -0.0477 S13: 0.0186 REMARK 3 S21: 0.0524 S22: -0.0009 S23: -0.0092 REMARK 3 S31: -0.0375 S32: 0.0443 S33: 0.0937 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 207:314)) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6363 6.6088 26.2283 REMARK 3 T TENSOR REMARK 3 T11: 0.7498 T22: 0.7299 REMARK 3 T33: 0.1140 T12: -0.0000 REMARK 3 T13: -0.1442 T23: 0.0969 REMARK 3 L TENSOR REMARK 3 L11: 0.0480 L22: 0.0538 REMARK 3 L33: 0.0347 L12: 0.0499 REMARK 3 L13: 0.0082 L23: 0.0074 REMARK 3 S TENSOR REMARK 3 S11: 0.0429 S12: 0.1345 S13: 0.0062 REMARK 3 S21: -0.0960 S22: -0.0167 S23: 0.0195 REMARK 3 S31: -0.0162 S32: -0.0205 S33: 0.0793 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 315:417)) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2770 4.6645 74.5689 REMARK 3 T TENSOR REMARK 3 T11: 0.1223 T22: 0.2089 REMARK 3 T33: -0.0511 T12: -0.2173 REMARK 3 T13: -0.0618 T23: 0.0647 REMARK 3 L TENSOR REMARK 3 L11: 0.1562 L22: 0.1720 REMARK 3 L33: 0.0214 L12: 0.1079 REMARK 3 L13: -0.0129 L23: 0.0095 REMARK 3 S TENSOR REMARK 3 S11: 0.0883 S12: -0.1495 S13: -0.0419 REMARK 3 S21: 0.1652 S22: -0.0875 S23: -0.0645 REMARK 3 S31: 0.0026 S32: 0.0352 S33: 0.0753 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC LIMITS WERE USED TO REMARK 3 TRUNCATE THE DATA REMARK 4 REMARK 4 5DZW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000214076. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14859 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.420 REMARK 200 RESOLUTION RANGE LOW (A) : 44.712 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.22000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 1.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5DZV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, MES, PH 6.2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 37.24000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.15500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.24000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.15500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C). REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 601 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 418 REMARK 465 VAL A 419 REMARK 465 ASN A 420 REMARK 465 ASP A 421 REMARK 465 HIS A 422 REMARK 465 HIS A 423 REMARK 465 HIS A 424 REMARK 465 HIS A 425 REMARK 465 HIS A 426 REMARK 465 HIS A 427 REMARK 465 HIS A 428 REMARK 465 HIS A 429 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 103 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 147 CG OD1 OD2 REMARK 470 TYR A 148 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 151 CG CD1 CD2 REMARK 470 LYS A 153 CG CD CE NZ REMARK 470 ASP A 157 CG OD1 OD2 REMARK 470 GLU A 158 CG CD OE1 OE2 REMARK 470 ARG A 159 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 161 CG CD CE NZ REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 ARG A 215 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 231 CG CD1 CD2 REMARK 470 LYS A 234 CG CD CE NZ REMARK 470 GLU A 242 CG CD OE1 OE2 REMARK 470 ASN A 259 CG OD1 ND2 REMARK 470 LYS A 261 CG CD CE NZ REMARK 470 TYR A 262 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 TYR A 278 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 285 CD CE NZ REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 LYS A 296 CE NZ REMARK 470 GLN A 298 CG CD OE1 NE2 REMARK 470 LYS A 306 CG CD CE NZ REMARK 470 GLU A 322 CG CD OE1 OE2 REMARK 470 ARG A 331 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 373 CG CD CE NZ REMARK 470 ASP A 385 CG OD1 OD2 REMARK 470 ARG A 386 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 387 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 18 90.30 -69.12 REMARK 500 ARG A 42 -81.69 -72.44 REMARK 500 LEU A 66 -76.91 -99.53 REMARK 500 ARG A 83 70.98 50.64 REMARK 500 ASN A 98 72.65 -69.89 REMARK 500 PRO A 145 74.99 -67.83 REMARK 500 HIS A 363 38.12 -85.41 REMARK 500 SER A 382 -174.36 58.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 505 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 8 OE2 REMARK 620 2 GLU A 64 OE2 102.6 REMARK 620 3 ASP A 96 OD2 87.1 139.3 REMARK 620 4 ILE A 97 O 77.6 129.0 91.6 REMARK 620 5 ASP A 99 OD1 82.8 70.1 150.5 59.3 REMARK 620 6 ASP A 132 OD1 163.5 65.6 109.4 100.3 82.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 506 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 8 OE1 REMARK 620 2 GLU A 8 OE2 44.8 REMARK 620 3 GLU A 9 OE2 80.4 116.9 REMARK 620 4 GLU A 64 OE1 69.8 76.9 116.7 REMARK 620 5 GLU A 64 OE2 111.2 84.9 154.6 52.6 REMARK 620 6 ASP A 99 OD1 117.9 76.6 120.8 122.5 75.0 REMARK 620 7 ASP A 99 OD2 115.9 102.6 71.3 171.5 119.0 49.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 507 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 98 OD1 REMARK 620 2 ASN A 100 O 88.7 REMARK 620 3 ASP A 130 OD1 157.3 70.3 REMARK 620 4 ASP A 130 OD2 155.5 115.2 45.0 REMARK 620 5 ASP A 132 OD2 71.7 90.3 115.6 111.3 REMARK 620 6 ASN A 136 O 89.7 157.0 106.1 66.3 110.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 508 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 115 OE1 REMARK 620 2 GLU A 174 OE2 110.5 REMARK 620 3 ASP A 205 OD1 97.0 79.7 REMARK 620 4 ALA A 206 O 89.7 154.1 81.9 REMARK 620 5 ASP A 208 OD1 71.4 134.4 145.8 66.4 REMARK 620 6 ASP A 241 OD1 163.2 70.6 99.7 94.9 95.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 509 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 115 OE2 REMARK 620 2 ASP A 172 OD1 68.9 REMARK 620 3 GLU A 174 OE1 95.0 77.3 REMARK 620 4 ASP A 208 OD1 88.3 143.8 134.3 REMARK 620 5 ASP A 208 OD2 67.2 95.0 162.1 49.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 510 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 207 OD1 REMARK 620 2 ASN A 209 O 108.1 REMARK 620 3 ASP A 239 OD2 159.0 91.5 REMARK 620 4 ASP A 241 OD2 68.9 85.4 121.6 REMARK 620 5 ASN A 245 O 94.6 156.8 66.7 98.8 REMARK 620 6 ASP A 295 OD2 79.2 92.8 92.8 145.6 96.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 511 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 224 OE2 REMARK 620 2 ASP A 280 OD1 59.5 REMARK 620 3 GLU A 282 OE1 106.5 78.5 REMARK 620 4 ASP A 316 OD1 93.5 153.0 114.1 REMARK 620 5 ASP A 316 OD2 66.3 111.3 158.7 49.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 512 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 224 OE1 REMARK 620 2 GLU A 282 OE1 89.1 REMARK 620 3 ASP A 313 OD1 104.3 93.4 REMARK 620 4 ILE A 314 O 91.1 172.6 93.8 REMARK 620 5 ASP A 316 OD1 85.9 108.2 156.5 64.5 REMARK 620 6 ASP A 349 OD1 156.9 90.3 98.8 86.6 72.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 513 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 315 OD1 REMARK 620 2 ASN A 317 O 101.8 REMARK 620 3 ASP A 347 OD1 168.8 84.3 REMARK 620 4 ASP A 347 OD2 137.2 104.1 47.9 REMARK 620 5 ASP A 349 OD2 68.6 94.8 101.7 140.8 REMARK 620 6 ASN A 353 O 79.3 170.3 96.3 69.8 94.6 REMARK 620 7 ASP A 400 OD2 69.5 84.5 120.8 79.7 137.0 87.0 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DZV RELATED DB: PDB REMARK 900 RELATED ID: 5DZX RELATED DB: PDB REMARK 900 RELATED ID: 5DZY RELATED DB: PDB DBREF 5DZW A 1 421 UNP O88689 PCDA4_MOUSE 30 450 SEQADV 5DZW HIS A 422 UNP O88689 EXPRESSION TAG SEQADV 5DZW HIS A 423 UNP O88689 EXPRESSION TAG SEQADV 5DZW HIS A 424 UNP O88689 EXPRESSION TAG SEQADV 5DZW HIS A 425 UNP O88689 EXPRESSION TAG SEQADV 5DZW HIS A 426 UNP O88689 EXPRESSION TAG SEQADV 5DZW HIS A 427 UNP O88689 EXPRESSION TAG SEQADV 5DZW HIS A 428 UNP O88689 EXPRESSION TAG SEQADV 5DZW HIS A 429 UNP O88689 EXPRESSION TAG SEQRES 1 A 429 GLN ILE HIS TYR SER ILE PRO GLU GLU ALA LYS HIS GLY SEQRES 2 A 429 THR PHE VAL GLY ARG ILE ALA GLN ASP LEU GLY LEU GLU SEQRES 3 A 429 LEU THR GLU LEU VAL PRO ARG LEU PHE ARG VAL ALA SER SEQRES 4 A 429 LYS ASP ARG GLY ASP LEU LEU GLU VAL ASN LEU GLN ASN SEQRES 5 A 429 GLY ILE LEU PHE VAL ASN SER ARG ILE ASP ARG GLU GLU SEQRES 6 A 429 LEU CYS GLY ARG SER ALA GLU CYS SER ILE HIS LEU GLU SEQRES 7 A 429 VAL ILE VAL ASP ARG PRO LEU GLN VAL PHE HIS VAL GLU SEQRES 8 A 429 VAL GLU VAL ARG ASP ILE ASN ASP ASN PRO PRO ARG PHE SEQRES 9 A 429 PRO THR THR GLN LYS ASN LEU PHE ILE ALA GLU SER ARG SEQRES 10 A 429 PRO LEU ASP THR TRP PHE PRO LEU GLU GLY ALA SER ASP SEQRES 11 A 429 ALA ASP ILE GLY ILE ASN ALA VAL LEU THR TYR ARG LEU SEQRES 12 A 429 SER PRO ASN ASP TYR PHE SER LEU GLU LYS PRO SER ASN SEQRES 13 A 429 ASP GLU ARG VAL LYS GLY LEU GLY LEU VAL LEU ARG LYS SEQRES 14 A 429 SER LEU ASP ARG GLU GLU THR PRO GLU ILE ILE LEU VAL SEQRES 15 A 429 LEU THR VAL THR ASP GLY GLY LYS PRO GLU LEU THR GLY SEQRES 16 A 429 SER VAL GLN LEU LEU ILE THR VAL LEU ASP ALA ASN ASP SEQRES 17 A 429 ASN ALA PRO VAL PHE ASP ARG SER LEU TYR THR VAL LYS SEQRES 18 A 429 LEU PRO GLU ASN VAL PRO ASN GLY THR LEU VAL VAL LYS SEQRES 19 A 429 VAL ASN ALA SER ASP LEU ASP GLU GLY VAL ASN GLY ASP SEQRES 20 A 429 ILE MET TYR SER PHE SER THR ASP ILE SER PRO ASN VAL SEQRES 21 A 429 LYS TYR LYS PHE HIS ILE ASP PRO VAL SER GLY GLU ILE SEQRES 22 A 429 ILE VAL LYS GLY TYR ILE ASP PHE GLU GLU CYS LYS SER SEQRES 23 A 429 TYR GLU ILE LEU ILE GLU GLY ILE ASP LYS GLY GLN LEU SEQRES 24 A 429 PRO LEU SER GLY HIS CYS LYS VAL ILE VAL GLN VAL GLU SEQRES 25 A 429 ASP ILE ASN ASP ASN VAL PRO GLU LEU GLU PHE LYS SER SEQRES 26 A 429 LEU SER LEU PRO ILE ARG GLU ASN SER PRO VAL GLY THR SEQRES 27 A 429 VAL ILE ALA LEU ILE SER VAL SER ASP ARG ASP THR GLY SEQRES 28 A 429 VAL ASN GLY GLN VAL THR CYS SER LEU THR SER HIS VAL SEQRES 29 A 429 PRO PHE LYS LEU VAL SER THR PHE LYS ASN TYR TYR SER SEQRES 30 A 429 LEU VAL LEU ASP SER ALA LEU ASP ARG GLU THR THR ALA SEQRES 31 A 429 ASP TYR LYS VAL VAL VAL THR ALA ARG ASP GLY GLY SER SEQRES 32 A 429 PRO SER LEU TRP ALA THR ALA SER VAL SER VAL GLU VAL SEQRES 33 A 429 ALA ASP VAL ASN ASP HIS HIS HIS HIS HIS HIS HIS HIS HET MAN A 501 11 HET MAN A 502 11 HET MAN A 503 11 HET NAG A 504 14 HET CA A 505 1 HET CA A 506 1 HET CA A 507 1 HET CA A 508 1 HET CA A 509 1 HET CA A 510 1 HET CA A 511 1 HET CA A 512 1 HET CA A 513 1 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 MAN 3(C6 H12 O6) FORMUL 5 NAG C8 H15 N O6 FORMUL 6 CA 9(CA 2+) FORMUL 15 HOH *10(H2 O) HELIX 1 AA1 ARG A 18 LEU A 23 1 6 HELIX 2 AA2 GLU A 26 VAL A 31 1 6 HELIX 3 AA3 ASP A 62 CYS A 67 1 6 HELIX 4 AA4 GLY A 134 ALA A 137 5 4 HELIX 5 AA5 GLU A 242 GLY A 246 5 5 HELIX 6 AA6 SER A 257 LYS A 263 1 7 HELIX 7 AA7 THR A 350 GLY A 354 5 5 SHEET 1 AA1 4 ILE A 2 PRO A 7 0 SHEET 2 AA1 4 GLN A 86 ARG A 95 1 O GLU A 93 N ILE A 6 SHEET 3 AA1 4 SER A 74 VAL A 81 -1 N LEU A 77 O VAL A 90 SHEET 4 AA1 4 ARG A 36 SER A 39 -1 N ARG A 36 O ILE A 80 SHEET 1 AA2 3 PHE A 15 GLY A 17 0 SHEET 2 AA2 3 ILE A 54 VAL A 57 -1 O LEU A 55 N GLY A 17 SHEET 3 AA2 3 LEU A 46 ASN A 49 -1 N GLU A 47 O PHE A 56 SHEET 1 AA3 4 GLN A 108 LEU A 111 0 SHEET 2 AA3 4 THR A 194 THR A 202 1 O THR A 202 N LEU A 111 SHEET 3 AA3 4 GLU A 178 ASP A 187 -1 N ILE A 179 O ILE A 201 SHEET 4 AA3 4 LEU A 139 LEU A 143 -1 N ARG A 142 O THR A 184 SHEET 1 AA4 2 PHE A 149 GLU A 152 0 SHEET 2 AA4 2 GLY A 164 LEU A 167 -1 O VAL A 166 N SER A 150 SHEET 1 AA5 2 VAL A 212 PHE A 213 0 SHEET 2 AA5 2 ALA A 237 SER A 238 -1 O SER A 238 N VAL A 212 SHEET 1 AA6 4 LEU A 217 LEU A 222 0 SHEET 2 AA6 4 SER A 302 VAL A 311 1 O LYS A 306 N TYR A 218 SHEET 3 AA6 4 SER A 286 ASP A 295 -1 N ILE A 291 O CYS A 305 SHEET 4 AA6 4 ILE A 248 PHE A 252 -1 N MET A 249 O ILE A 294 SHEET 1 AA7 3 LEU A 231 LYS A 234 0 SHEET 2 AA7 3 GLU A 272 VAL A 275 -1 O ILE A 273 N VAL A 233 SHEET 3 AA7 3 PHE A 264 ILE A 266 -1 N HIS A 265 O ILE A 274 SHEET 1 AA8 4 GLU A 320 LEU A 326 0 SHEET 2 AA8 4 VAL A 339 SER A 346 -1 O SER A 346 N GLU A 320 SHEET 3 AA8 4 TYR A 375 VAL A 379 -1 O TYR A 376 N ILE A 343 SHEET 4 AA8 4 LYS A 367 PHE A 372 -1 N LYS A 367 O VAL A 379 SHEET 1 AA9 4 ILE A 330 ARG A 331 0 SHEET 2 AA9 4 TRP A 407 ALA A 417 1 O ALA A 417 N ILE A 330 SHEET 3 AA9 4 ASP A 391 ASP A 400 -1 N ALA A 398 O ALA A 408 SHEET 4 AA9 4 VAL A 356 LEU A 360 -1 N THR A 357 O ARG A 399 SSBOND 1 CYS A 67 CYS A 73 1555 1555 2.03 LINK ND2 ASN A 236 C1 NAG A 504 1555 1555 1.45 LINK OG1 THR A 409 C1 MAN A 501 1555 1555 1.44 LINK OG SER A 411 C1 MAN A 502 1555 1555 1.44 LINK OG SER A 413 C1 MAN A 503 1555 1555 1.44 LINK OE2 GLU A 8 CA CA A 505 1555 1555 2.39 LINK OE1 GLU A 8 CA CA A 506 1555 1555 2.56 LINK OE2 GLU A 8 CA CA A 506 1555 1555 3.07 LINK OE2 GLU A 9 CA CA A 506 1555 1555 3.06 LINK OE2 GLU A 64 CA CA A 505 1555 1555 2.43 LINK OE1 GLU A 64 CA CA A 506 1555 1555 2.47 LINK OE2 GLU A 64 CA CA A 506 1555 1555 2.47 LINK OD2 ASP A 96 CA CA A 505 1555 1555 2.36 LINK O ILE A 97 CA CA A 505 1555 1555 2.56 LINK OD1 ASN A 98 CA CA A 507 1555 1555 2.51 LINK OD1 ASP A 99 CA CA A 505 1555 1555 2.98 LINK OD1 ASP A 99 CA CA A 506 1555 1555 2.69 LINK OD2 ASP A 99 CA CA A 506 1555 1555 2.51 LINK O ASN A 100 CA CA A 507 1555 1555 2.50 LINK OE1 GLU A 115 CA CA A 508 1555 1555 3.11 LINK OE2 GLU A 115 CA CA A 509 1555 1555 2.44 LINK OD1 ASP A 130 CA CA A 507 1555 1555 3.06 LINK OD2 ASP A 130 CA CA A 507 1555 1555 2.53 LINK OD1 ASP A 132 CA CA A 505 1555 1555 3.18 LINK OD2 ASP A 132 CA CA A 507 1555 1555 2.95 LINK O ASN A 136 CA CA A 507 1555 1555 2.72 LINK OD1 ASP A 172 CA CA A 509 1555 1555 3.04 LINK OE2 GLU A 174 CA CA A 508 1555 1555 2.54 LINK OE1 GLU A 174 CA CA A 509 1555 1555 2.44 LINK OD1 ASP A 205 CA CA A 508 1555 1555 2.46 LINK O ALA A 206 CA CA A 508 1555 1555 2.37 LINK OD1 ASN A 207 CA CA A 510 1555 1555 2.66 LINK OD1 ASP A 208 CA CA A 508 1555 1555 2.85 LINK OD1 ASP A 208 CA CA A 509 1555 1555 2.57 LINK OD2 ASP A 208 CA CA A 509 1555 1555 2.68 LINK O ASN A 209 CA CA A 510 1555 1555 2.45 LINK OE2 GLU A 224 CA CA A 511 1555 1555 2.50 LINK OE1 GLU A 224 CA CA A 512 1555 1555 2.90 LINK OD2 ASP A 239 CA CA A 510 1555 1555 2.37 LINK OD1 ASP A 241 CA CA A 508 1555 1555 2.64 LINK OD2 ASP A 241 CA CA A 510 1555 1555 2.87 LINK O ASN A 245 CA CA A 510 1555 1555 2.58 LINK OD1 ASP A 280 CA CA A 511 1555 1555 2.99 LINK OE1 GLU A 282 CA CA A 511 1555 1555 2.44 LINK OE1 GLU A 282 CA CA A 512 1555 1555 2.57 LINK OD2 ASP A 295 CA CA A 510 1555 1555 2.77 LINK OD1 ASP A 313 CA CA A 512 1555 1555 2.47 LINK O ILE A 314 CA CA A 512 1555 1555 2.67 LINK OD1 ASN A 315 CA CA A 513 1555 1555 2.53 LINK OD1 ASP A 316 CA CA A 511 1555 1555 2.58 LINK OD2 ASP A 316 CA CA A 511 1555 1555 2.68 LINK OD1 ASP A 316 CA CA A 512 1555 1555 2.63 LINK O ASN A 317 CA CA A 513 1555 1555 2.51 LINK OD1 ASP A 347 CA CA A 513 1555 1555 2.58 LINK OD2 ASP A 347 CA CA A 513 1555 1555 2.80 LINK OD1 ASP A 349 CA CA A 512 1555 1555 2.79 LINK OD2 ASP A 349 CA CA A 513 1555 1555 2.56 LINK O ASN A 353 CA CA A 513 1555 1555 2.54 LINK OD2 ASP A 400 CA CA A 513 1555 1555 2.75 CISPEP 1 ARG A 83 PRO A 84 0 -6.30 CISPEP 2 LYS A 190 PRO A 191 0 2.00 CISPEP 3 LEU A 328 PRO A 329 0 0.55 CISPEP 4 SER A 403 PRO A 404 0 0.52 CRYST1 74.480 56.310 173.670 90.00 99.05 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013426 0.000000 0.002139 0.00000 SCALE2 0.000000 0.017759 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005831 0.00000